thank you very much Sean, this is exactly what I needed!

On Fri, Sep 17, 2010 at 1:26 PM, Sean Davis <sdavis2@mail.nih.gov> wrote:

>
>
> On Fri, Sep 17, 2010 at 1:17 PM, Sunny Srivastava <research.baba@gmail.com
> > wrote:
>
>> Dear Dr. Huber,
>> Thanks for your reply, but I had looked at this function. What I
>> understood
>> from the documentation was: if give the height at which I want to cut,
>> then
>> it gives me $upper and $lower, but I guess I have to "hack" to get the
>> height which gives me a specific number of clusters?
>>
>> I am I thinking correctly?
>>
>>
> You could also try the cutree() function.
>
> Sean
>
>
>> On Fri, Sep 17, 2010 at 10:11 AM, Wolfgang Huber <whuber@embl.de> wrote:
>>
>> > Sunny
>> >
>> > the function "cut.dendrogram" from the "stats" package does what you
>> want.
>> > It's described in the manual page of the "dendrogram" class. Try typing,
>> in
>> > R:
>> >
>> >  ? dendrogram
>> >
>> > Best wishes
>> >        Wolfgang
>> >
>> >
>> >
>> >
>> > On Sep/16/10 12:57 PM, Sunny Srivastava wrote:
>> >
>> >> Hello Bioconductor Helpers,
>> >> I have a question about extracting the clusters of genes after we make
>> the
>> >> heatmap (say ht4) using the heatmap.2 function. Basically, I want to
>> get
>> >> the
>> >> clusters which are shown as row dendrogram in the heatmap.
>> >>
>> >> I understand that ht4$rowDendrogram is an object of dendrogram and it
>> >> containes details of all the nodes and branches, but lets say I want to
>> >> know
>> >> the number of clusters and the genes in each cluster if I terminated
>> the
>> >> tree (dendrogram) at a particular height. Also, if I know that I want
>> 12
>> >> clusters, how do I know which height I should terminate the tree (or
>> >> branching structure)
>> >>
>> >> I am sorry I am not clear. Please let me know if you need any further
>> >> clarifications. Thanks in advance for your help.
>> >>
>> >> Best Regards,
>> >> S.
>> >>
>> >>
>> >> Below is the dump of the matrix *row.scaled.fc2* and the object *ht4*
>> >> which
>> >> was obtained by using the heatmap.2 function.
>> >>
>> >>  --
>> >
>> >
>> > Wolfgang Huber
>> > EMBL
>> > http://www.embl.de/research/units/genome_biology/huber
>> >
>> >
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